read_coverage {DegNorm} | R Documentation

## Function to calculate read coverage score for one bam file

### Description

This function judges whether bam file is single-end and paired-end, and generate bam file index if needed. It calls function `paired_end_cov_by_ch` or `single_end_by_ch`. It takes multiple-core structure for parallel computing for efficiency.

### Usage

    read_coverage(bam_file,all_genes,cores)

### Arguments

`bam_file` | The name of the bam file.
`all_genes` | An GRangesList object. It's the parsed genes annotation file from GTF file.
`cores` | number of cores to use.

### Details

This function judges whether bam file is single-end and paired-end, and generate bam file index if needed. It takes multiple-core structure for parallel computing for efficiency.

### Value

This function returns a coverageClass object. It contains a list of: (1) a list of coverage score for each gene in RLE format and (2) a dataframe for read counts

### See Also

`read_coverage_batch`

[Package DegNorm version 1.0.0 Index]